Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

• Published in: Virus evolution Vol. 7; no. 2; p. veab051
• Main Authors: Gutierrez, Bernardo, Márquez, Sully, Prado-Vivar, Belén, Becerra-Wong, Mónica, Guadalupe, Juan José, Candido, Darlan Da Silva, Fernandez-Cadena, Juan Carlos, Morey-Leon, Gabriel, Armas-Gonzalez, Rubén, Andrade-Molina, Derly Madeleiny, Bruno, Alfredo, De Mora, Domenica, Olmedo, Maritza, Portugal, Denisse, Gonzalez, Manuel, Orlando, Alberto, Drexler, Jan Felix, Moreira-Soto, Andres, Sander, Anna-Lena, Brünink, Sebastian, Kühne, Arne, Patiño, Leandro, Carrazco-Montalvo, Andrés, Mestanza, Orson, Zurita, Jeannete, Sevillano, Gabriela, Du Plessis, Louis, McCrone, John T, Coloma, Josefina, Trueba, Gabriel, Barragán, Verónica, Rojas-Silva, Patricio, Grunauer, Michelle, Kraemer, Moritz U G, Faria, Nuno R, Escalera-Zamudio, Marina, Pybus, Oliver G, Cárdenas, Paúl
• Format: Journal Article
• Language: English
• Published: UK Oxford University Press 01.11.2021
• Subjects: molecular epidemiology; phylogenetics; SARS-CoV-2; transmission lineages; phylogeography
• ISSN: 2057-1577; 2057-1577
• DOI: 10.1093/ve/veab051

Abstract Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.